The self-limiting dynamics of TGF-ß signaling in silico and in vitro, with negative feedback through PPM1A upregulation.

The TGF-ß/Smad signaling system decreases its activity through strong negative regulation. Several molecular mechanisms of negative regulation have been published, but the relative impact of each mechanism on the overall system is unknown. In this work, we used computational and experimental methods to assess multiple negative regulatory effects on Smad signaling in HaCaT cells. Previously reported negative regulatory effects were classified by time-scale: degradation of phosphorylated R-Smad and I-Smad-induced receptor degradation were slow-mode effects, and dephosphorylation of R-Smad was a fast-mode effect. We modeled combinations of these effects, but found no combination capable of explaining the observed dynamics of TGF-ß/Smad signaling. We then proposed a negative feedback loop with upregulation of the phosphatase PPM1A. The resulting model was able to explain the dynamics of Smad signaling, under both short and long exposures to TGF-ß. Consistent with this model, immuno-blots showed PPM1A levels to be significantly increased within 30 min after TGF-ß stimulation. Lastly, our model was able to resolve an apparent contradiction in the published literature, concerning the dynamics of phosphorylated R-Smad degradation. We conclude that the dynamics of Smad negative regulation cannot be explained by the negative regulatory effects that had previously been modeled, and we provide evidence for a new negative feedback loop through PPM1A upregulation. This work shows that tight coupling of computational and experiments approaches can yield improved understanding of complex pathways.

Hidden leprosy cases in tribal population groups and how to reach them through a collaborative effort.

BACKGROUND: Tribal populations are an underserved population group and access to health services is a major challenge for them. Since leprosy treatment is integrated with the general health services, identifying leprosy cases is not be easy in these settings and they remain as endemic reservoirs, unless greater efforts are made to reach them. METHODOLOGY: An active search operation was conducted in the tribal colonies in four pre-identified Health & Nutrition Clusters, Nellore district, Andhra Pradesh, India, in 2013. After a brief training, village health nurses and selected volunteers covered all the households, showing flash cards with photos of leprosy cases and enquiring if there was any resident with a similar condition. Suspects were listed and examined by the district leprosy supervisor and field coordinators from Damien Foundation. Follow up interviews were done after one year to assess the treatment completion rate. RESULTS: Village health workers covered 47,574 people living in the tribal colonies and identified 325 leprosy suspects. Among them, 70 were confirmed as new leprosy cases. The prevalence of previously undetected leprosy cases was found to be 14.7/10,000. Out of 70 cases, 19 (27%) were children, 35 (50%) were female, 32 (45.7%) were classified as MB leprosy, 6 (8.6%) had a leprosy reaction and 11 (15.7%) persons had Grade 2 disability at the time of diagnosis. The treatment completion rate was found to be 74% at the end of one year. CONCLUSION: The study reveals a very high burden of leprosy among the tribal population and demonstrates how resources can be mobilized from government, NGO and local community sources to promote early case detection among underserved population groups.

Approximate probabilistic analysis of biopathway dynamics.

MOTIVATION: Biopathways are often modeled as systems of ordinary differential equations (ODEs). Such systems will usually have many unknown parameters and hence will be difficult to calibrate. Since the data available for calibration will have limited precision, an approximate representation of the ODEs dynamics should suffice. One must, however, be able to efficiently construct such approximations for large models and perform model calibration and subsequent analysis. RESULTS: We present a graphical processing unit (GPU) based scheme by which a system of ODEs is approximated as a dynamic Bayesian network (DBN). We then construct a model checking procedure for DBNs based on a simple probabilistic linear time temporal logic. The GPU implementation considerably extends the reach of our previous PC-cluster-based implementation (Liu et al., 2011b). Further, the key components of our algorithm can serve as the GPU kernel for other Monte Carlo simulations-based analysis of biopathway dynamics. Similarly, our model checking framework is a generic one and can be applied in other systems biology settings. We have tested our methods on three ODE models of bio-pathways: the epidermal growth factor-nerve growth factor pathway, the segmentation clock network and the MLC-phosphorylation pathway models. The GPU implementation shows significant gains in performance and scalability whereas the model checking framework turns out to be convenient and efficient for specifying and verifying interesting pathways properties. AVAILABILITY: The source code is freely available at http://www.comp.nus.edu.sg/~rpsysbio/pada-gpu/

Improved statistical model checking methods for pathway analysis.

Statistical model checking techniques have been shown to be effective for approximate model checking on large stochastic systems, where explicit representation of the state space is impractical. Importantly, these techniques ensure the validity of results with statistical guarantees on errors. There is an increasing interest in these classes of algorithms in computational systems biology since analysis using traditional model checking techniques does not scale well. In this context, we present two improvements to existing statistical model checking algorithms. Firstly, we construct an algorithm which removes the need of the user to define the indifference region, a critical parameter in previous sequential hypothesis testing algorithms. Secondly, we extend the algorithm to account for the case when there may be a limit on the computational resources that can be spent on verifying a property; i.e, if the original algorithm is not able to make a decision even after consuming the available amount of resources, we resort to a p-value based approach to make a decision. We demonstrate the improvements achieved by our algorithms in comparison to current algorithms first with a straightforward yet representative example, followed by a real biological model on cell fate of gustatory neurons with microRNAs.

A computational and experimental study of the regulatory mechanisms of the complement system.

The complement system is key to innate immunity and its activation is necessary for the clearance of bacteria and apoptotic cells. However, insufficient or excessive complement activation will lead to immune-related diseases. It is so far unknown how the complement activity is up- or down- regulated and what the associated pathophysiological mechanisms are. To quantitatively understand the modulatory mechanisms of the complement system, we built a computational model involving the enhancement and suppression mechanisms that regulate complement activity. Our model consists of a large system of Ordinary Differential Equations (ODEs) accompanied by a dynamic Bayesian network as a probabilistic approximation of the ODE dynamics. Applying Bayesian inference techniques, this approximation was used to perform parameter estimation and sensitivity analysis. Our combined computational and experimental study showed that the antimicrobial response is sensitive to changes in pH and calcium levels, which determines the strength of the crosstalk between CRP and L-ficolin. Our study also revealed differential regulatory effects of C4BP. While C4BP delays but does not decrease the classical complement activation, it attenuates but does not significantly delay the lectin pathway activation. We also found that the major inhibitory role of C4BP is to facilitate the decay of C3 convertase. In summary, the present work elucidates the regulatory mechanisms of the complement system and demonstrates how the bio-pathway machinery maintains the balance between activation and inhibition. The insights we have gained could contribute to the development of therapies targeting the complement system.

Immune interferon and leukocyte-conditioned medium induce normal and leukemic myeloid cells to differentiate along the monocytic pathway.

Conditioned medium from phytohemagglutinin-stimulated human leukocytes contains a factor that can induce promyelocytic cell lines and certain acute myelogenous leukemia cells to differentiate along the monocytic pathway. In this report, we show that immature myeloid cells from normal bone marrow or the peripheral blood of patients with chronic myelogenous leukemia can be induced to differentiate to monocyte-like cells by immune gamma interferon (IFN gamma). We have identified IFN gamma as the predominant differentiation factor contained in the conditioned medium. Purified or recombinant IFN gamma, but not various preparations of IFN alpha or beta, can induce monocytic differentiation in myeloid cells. In cultures containing conditioned medium, the cells fail to continue myeloid maturation, and are induced to express monocyte markers and functions, such as monocyte-specific surface antigens, HLA-DR antigens, Fc receptors for monomeric immunoglobulins, nonspecific esterase, and the ability to mediate antibody-dependent, cell-mediated cytotoxicity. Even myeloid cells as mature as metamyelocytes or band cells can be induced by IFN gamma to undergo monocyte differentiation, but monocyte-specific or HLA-DR antigens are not induced in mature neutrophils. These findings reveal a previously unknown, specific function of human IFN gamma and offer new insights to the regulation of monocyte recruitment and differentiation during a virus infection or immune response.

The platelet glycoprotein IIb/IIIa-like protein in human endothelial cells promotes adhesion but not initial attachment to extracellular matrix.

On platelets the membrane glycoprotein IIb/IIIa complex (GPIIb/IIIa) functions in adhesive interactions with fibrinogen, von Willebrand factor, and fibronectin. However, the function of GPIIb/IIIa-like proteins on endothelial cells, as well as the ligand(s) the complex binds, is unknown. Using a highly specific polyclonal antibody we have explored the function of GPIIb/IIIa-like proteins on human umbilical vein endothelial cells (HUVE). Analysis by immunoblotting shows that this antiserum recognizes the endothelial GPIIIa-like protein of the complex. The IgG fraction of the polyclonal antiserum and its Fab' fragments detach confluent and subconfluent HUVE from extracellular substrata. The effect of the anti-GPIIb/IIIa IgG is not toxic as the detached cells maintain their viability after trypsinization and replating. Anti-GPIIb/IIIa IgG does not inhibit HUVE binding to extracellular matrix or purified fibronectin in an attachment assay despite the presence of intact GPIIb/IIIa on HUVE detached from substrate by various methods. Apparently, the GPIIb/IIIa-like protein on HUVE is important in normal HUVE adhesion to the extracellular matrix, but it is not required in the initial attachment of HUVE to extracellular matrix.

Monoclonal immunoglobulin M lambda coagulation inhibitor with phospholipid specificity. Mechanism of a lupus anticoagulant.

Prolongation of all phospholipid-dependent coagulation tests was found in a patient with macroglobulinemia, despite absence of bleeding manifestations. The purified monoclonal IgM lambda protein and its Fabmu tryptic fragment induced similar changes in normal plasma. Patient IgM and Fabmu completely inhibited Ca++-dependent binding of radiolabeled prothrombin and Factor X to mixed phospholipid micelles. The patient's IgM lambda paraprotein reacted with phosphatidylserine and, to a lesser extent, with phosphatidylinositol and phosphatidic acid, but not with phosphatidylcholine or phosphatidylethanolamine. Prior incubation of phospholipid with patient Fabmu blocked the positive reactions. Substitution of washed platelets for phospholipid led to normalization of patient coagulation tests and corrected all abnormalities produced in normal plasma by patient IgM. Furthermore, binding of 125I-Factor Xa to thrombin-treated platelets was entirely normal in the presence of patient IgM. These studies support the concept that platelets, rather than phospholipid micelles, are the primary locus of prothrombin and Factor X activation in normal hemostasis.

A monoclonal antibody to human platelet glycoprotein IIIa detects a related protein in cultured human endothelial cells.

We have previously described a series of monoclonal antibodies against platelet membrane glycoproteins. Two of the antibodies, B59.2 and B2.12, recognize the glycoprotein IIb-IIIa complex. These two antibodies react specifically with glycoprotein (GP) IIIa, as shown by immunoblotting of sodium dodecyl sulfate-polyacrylamide gels of solubilized platelet membranes. Monoclonal B2.12, but not B59.2, binds to cultured human endothelial cells obtained from umbilical vein, internal iliac artery, and inferior vena cava. At saturation approximately 100,000 binding sites were detected per human umbilical vein endothelial cell. When solubilized radioiodinated cells were chromatographed on a column of agarose-bound B2.12, a single radiolabeled protein was obtained whose apparent molecular weight is slightly larger than that of platelet GP IIIa. This protein incorporated [35S]methionine when endothelial cells were labeled metabolically. These results demonstrate that human endothelial cell membranes synthesize a protein immunologically related to platelet GP IIIa.

Fibrinogen-independent platelet adhesion and thrombus formation on subendothelium mediated by glycoprotein IIb-IIIa complex at high shear rate.

Platelet adhesion and thrombus formation on subendothelium, studied at a shear rate of 2,600 s-1, were inhibited by two synthetic peptides known to interact with GPIIb-IIIa. One peptide (HHLGGAKQAGDV) corresponds to the carboxyl terminal segment of the fibrinogen gamma-chain (gamma 400-411) and the other (RGDS) contains the amino acid sequence Arg-Gly-Asp (RGD) common to fibronectin, von Willebrand factor, vitronectin and the alpha-chain of fibrinogen. Neither platelet adhesion nor thrombus formation were decreased in a patient with severe congenital fibrinogen deficiency and this was equally true when his blood was further depleted of the small amounts of fibrinogen present utilizing an anti-fibrinogen antibody. In normal subjects, adhesion and thrombus formation were inhibited by the Fab' fragments of a monoclonal anti-GPIIb-IIIa antibody (LJ-CP8), which interferes with the interaction of platelets with all four adhesive proteins in both the fluid and solid phase. However, another anti-GPIIb-IIIa antibody (LJ-P5) that had minimal effects on the interaction of platelets with fibrinogen, but inhibited to varying degrees platelet interaction with other adhesive proteins, was equally effective. The findings demonstrate that, at a shear rate of 2,600 s-1, adhesive proteins other than fibrinogen are involved in GPIIb-IIIa-mediated platelet adhesion and thrombus formation on subendothelium. In addition, since LJ-P5 inhibited the binding of soluble von Willebrand factor and vitronectin, these adhesive proteins may be involved in platelet thrombus formation. In contrast to the results obtained at a shear rate of 2,600 s-1, fibrinogen could play a role in mediating platelet-platelet interactions with weak agonists or lower shear rates.

Microvesicle-associated tissue factor and Trousseau's syndrome.

BACKGROUND: Trousseau's syndrome is a prothrombotic state associated with malignancy that is poorly understood pathophysiologically. METHODS AND RESULTS: Here we report studies on the blood of a 55-year-old man with giant-cell lung carcinoma who developed a severe form of Trousseau's syndrome. His clinical course was dominated by an extremely hypercoagulable state. Despite receiving potent antithrombotic therapy, he suffered eleven major arterial and venous thrombotic events over a 5 month period. We examined the patient's blood for tissue factor (TF), the major initiator of coagulation, and found its concentration in his plasma to be forty-one-fold higher than the mean concentration derived from testing of 16 normal individuals. CONCLUSION: Almost all of the TF in the patient's plasma was associated with cell-derived microvesicles, likely shed by the cancer cells.

A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk.

Parameter estimation is a critical problem in modeling biological pathways. It is difficult because of the large number of parameters to be estimated and the limited experimental data available. In this paper, we propose a decompositional approach to parameter estimation. It exploits the structure of a large pathway model to break it into smaller components, whose parameters can then be estimated independently. This leads to significant improvements in computational efficiency. We present our approach in the context of Hybrid Functional Petri Net modeling and evolutionary search for parameter value estimation. However, the approach can be easily extended to other modeling frameworks and is independent of the search method used. We have tested our approach on a detailed model of the Akt and MAPK pathways with two known and one hypothesized crosstalk mechanisms. The entire model contains 84 unknown parameters. Our simulation results exhibit good correlation with experimental data, and they yield positive evidence in support of the hypothesized crosstalk between the two pathways.

Gelatinous Marrow Transformation Associated with Imatinib: Case Report and Literature Review.

Gelatinous marrow transformation (GMT) is a rare condition observed in severe illness or malnutrition, in which the bone marrow contains amorphous "gelatinous" extracellular material, and histopathology demonstrates varied degrees of fat cell atrophy and loss of hematopoietic elements. An association of GMT with imatinib use in chronic myeloid leukemia (CML) has been reported recently. The objective of this study is to describe a case of GMT associated with imatinib use and review the existing similar cases in the literature to identify epidemiological patterns and potential imatinib-induced mechanisms leading to gelatinous conversion.

Innate immune memory and homeostasis may be conferred through crosstalk between the TLR3 and TLR7 pathways.

Toll-like receptors (TLRs) recognize pathogen-associated molecular patterns (PAMPs) and stimulate the innate immune response through the production of cytokines. The innate immune response depends on the timing of encountering PAMPs, suggesting a short-term "memory." In particular, activation of TLR3 appears to prime macrophages for the subsequent activation of TLR7, which leads to synergistically increased production of cytokines. By developing a calibrated mathematical model for the kinetics of TLR3 and TLR7 pathway crosstalk and providing experimental validation, we demonstrated the involvement of the Janus-activated kinase (JAK)-signal transducer and activator of transcription (STAT) pathway in controlling the synergistic production of cytokines. Signaling through this pathway played a dual role: It mediated the synergistic production of cytokines, thus boosting the immune response, and it also maintained homeostasis to avoid an excessive inflammatory response. Thus, we propose that the JAK-STAT pathway provides a cytokine rheostat mechanism, which enables macrophages to fine-tune their responses to multiple, temporally separated infection events involving the TLR3 and TLR7 pathways.

A human erythroleukemia cell line synthesizes a functionally active glycoprotein IIb-IIIa complex capable of binding fibrinogen.

The human erythroleukemia (HEL) cell line is known to express a number of platelet-megakaryocyte markers, including glycoproteins IIb and IIIa. Using [35S]methionine as well as monoclonal and polyclonal antibodies to glycoprotein IIb and IIIa, we have demonstrated synthesis of these two glycoproteins by this cell line. When Triton X-100-solubilized membranes were subjected to cross immunoelectrophoresis in 1% agarose, using a mixture of polyclonal antibodies to glycoproteins IIb and IIIa, a single peak was seen in the presence of Ca2+, whereas two distinct peaks were seen in the presence of 5 mM EDTA. When these crossed immunoelectrophoresis were overlaid with 125I-labelled fibrinogen, binding of fibrinogen to the glycoprotein IIb and IIIa complex peak was observed. When either the electrophoresis or the subsequent overlay was done in the presence of 5 mM EDTA, no 125I-fibrinogen binding was observed. These studies demonstrate that HEL cells contain glycoproteins IIb and IIIa capable of forming a Ca2+-dependent complex and capable of binding fibrinogen in a Ca2+-dependent reaction. Nevertheless, glycoprotein IIb- and IIIa-specific fibrinogen binding, of the type observed in platelets, could not be demonstrated in 'resting' or 'stimulated' intact HEL cells. The mechanism giving rise to this difference is currently unknown.

A modified Arg-Asp-Val (RDV) peptide derived during the synthesis of Arg-Glu-Asp-Val (REDV), a tetrapeptide derived from an alternatively spliced site in fibronectin, inhibits the binding of fibrinogen, fibronectin, von Willebrand factor and vitronectin to activated platelets.

Characterization of a side-product obtained during the synthesis of Arg-Glu-Asp-Val (REDV) with inhibitory activity in thrombin-activated platelet aggregation was carried out. The semipreparative column fractionation of REDV peptide was rechromatographed on an analytical HPLC column and revealed two peaks which were re-tested for inhibitory activity. Using amino acid analysis with sequencing and fast atom bombardment mass spectrometry (FABMS), the first peak was determined to be REDV with molecular mass of 517 Da, and the second peak was determined to be a modified RDV with a mass of 608 Da. The modified RDV peptide inhibited thrombin-induced platelet aggregation with an IC50 of 200 microM, and complete inhibition occurred at 600 microM. However, the REDV peptide did not inhibit platelet aggregation up to 1 mM concentration. The modified RDV peptide eluted platelet glycoprotein IIb-IIIa complex that had been bound to GRGDSP-agarose. These studies show that the modified RDV peptide interacts with the platelet glycoprotein IIb-IIIa complex. Based on the collision-induced dissociation (CID) mass spectral data analysis, the modified RDV peptide has been characterized to contain an N-terminus blocking group on the Arg residue. The origin of this blocking group is presumed to have originated from decomposition products of the phenylacetamidomethyl (PAM) resin used in the solid-phase synthesis of the target peptide Arg-Glu-Asp-Val.

Role for sulfatides in platelet aggregation.

BACKGROUND: Sulfatides are sulfated glycosphingolipids present on the surface of oligodendrocytes, renal tubular cells, and certain tumor cells. They appear to be involved in nerve conduction and cell adhesion, but their precise physiological function is not known. METHODS AND RESULTS: Here, we show a novel role for sulfatides as a major ligand for P-selectin in platelet adhesion and aggregation. Sulfatides are expressed on the platelet surface, and platelets expressing sulfatides adhere to P-selectin. Both sulfatide micelles and sulfatide-binding recombinant malaria circumsporozoite protein (MCSP) inhibit this adhesion. In parallel, platelets and CHO cells expressing P-selectin adhere to sulfatides, and anti-P-selectin antibodies inhibit this adhesion. Furthermore, both anti-P-selectin antibodies and sulfatide antagonist MCSP significantly reverse platelet aggregation induced by ADP, collagen, or thrombin receptor-activating peptide, suggesting that sulfatide-P-selectin interactions are necessary for the formation of stable platelet aggregates. CONCLUSIONS: These results show that sulfatide interactions with P-selectin are important in platelet adhesion and platelet aggregation. The sulfatide interactions with P-selectin stabilize platelet aggregates, representing a new mechanism of platelet aggregation that may play a significant role in hemostasis and thrombosis.

P-selectin expression on platelets determines size and stability of platelet aggregates.

BACKGROUND: P-selectin mediates rolling of platelets and leukocytes on activated endothelial cells. After platelet activation, P-selectin is translocated from intracellular granules to the external membrane, whereas fibrinogen aggregates platelets by bridging glycoprotein (GP) IIb/IIIa between adjacent platelets. METHODS AND RESULTS: In this study, we define a novel role for P-selectin in platelet aggregation. Expression of P-selectin on the platelet surface correlated strongly with the mean platelet aggregate size. Inhibition of P-selectin binding to its ligand by either monoclonal anti-P-selectin antibodies directed against the lectin domain or soluble human P-selectin reversed platelet aggregation even when added up to 5 minutes after activation; however, fibrinogen binding to platelets was not affected. This deaggregating effect significantly reduced the maximal size and number of platelet aggregates. When added 1 minute after platelet activation, anti-P-selectin antibody achieved 95% to 100% of the deaggregating effect of EDTA, whereas the anti-GP IIb/IIIa antibody abciximab had no effect. Monoclonal antibodies against known P-selectin ligands, such as P-selectin GP ligand-1 (PSGL-1) or GP Ib, had no effect on platelet aggregation, suggesting a different ligand for P-selectin in platelet aggregate stabilization. In kinetic studies, P-selectin was maximally expressed 10 minutes after platelet activation, whereas maximal activation of GP IIb/IIIa occurred within the first 10 seconds, suggesting that P-selectin operates after fibrinogen binding to activated GP IIb/IIIa. CONCLUSIONS: These results indicate that P-selectin interaction with a ligand, different from PSGL-1 or GP Ib, stabilizes initial GP IIb/IIIa-fibrinogen interactions, allowing the formation of large stable platelet aggregates.

Sulfatides: targets for anti-phospholipid antibodies.

BACKGROUND: Sulfatides are sulfated glycosphingolipids expressed on the surface of erythrocytes, leukocytes, and platelets. Sulfatides interact with several cell adhesion molecules involved in hemostasis. Beta2-glycoprotein I is an anionic phospholipid-binding plasma protein, and the phospholipid-bound form is the target for most anti-phospholipid antibodies that are associated with recurrent thrombosis, miscarriages, and neurological symptoms. In this study, we examined whether beta2-glycoprotein I forms a complex with sulfatides and thereby becomes a target for anti-phospholipid antibodies. METHODS AND RESULTS: Beta2-glycoprotein I binds to surface-bound sulfatides but not to other glycolipids, such as ceramide, cerebrosides, sphingomyelin, or ganglioside. At a sulfatide coating density of 1 microg/well, beta2-glycoprotein I reaches half-maximal binding at 2.5 microg/mL, and the binding is saturated at 10 microg/mL. The binding of beta2-glycoprotein I also depends on the coating density of sulfatides in the well. At a constant beta2-glycoprotein I concentration of 5 microg/mL, maximal binding of beta2-glycoprotein I is observed at a coating density of 1 mug/well. The serum from 14 patients with anti-cardiolipin antibodies, a subset of anti-phospholipid antibodies, bound to sulfatide-bound beta2-glycoprotein I and previous absorption on cardiolipin-coated surfaces decreased the immunoreactivity toward sulfatide-beta2-glycoprotein I complex by >50% in 12 of 14 patients. Furthermore, immunoaffinity-purified anti-cardiolipin antibodies from 4 of 5 patients reacted with sulfatide-bound beta2-glycoprotein I. CONCLUSIONS: These results show that not only anionic phospholipids, as commonly known, but also sulfatides are targets for most anti-phospholipid antibodies. We therefore postulate that interactions of these antibodies with sulfatides may contribute to some of the clinical symptoms of the anti-phospholipid antibody syndrome.